[Chimera-users] PDB model merging

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 26 09:12:27 PDT 2012

Hi Nikolay,
PDB files written from Chimera *do* preserve helix and strand assignments, so if you read them back into Chimera the secondary structures will be the same.  I just doublechecked that this is true even after combining models.

Also, since Chimera 1.5 (Dec 2010), you can read PQR format into Chimera.

Have you checked to make sure that the PDB2PQR step does not remove the secondary structure records?

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 25, 2012, at 3:11 PM, Nikolay Igorovich Rodionov wrote:

> Hi Eric,
> I am only concerned with preserving records that are involved in various renderings of each subunit. I am taking the combination pdb file and assigning partial charges to the residues using pdb2pqr and then rendering  the resulting pqr file in VMD because Chimera does not support pqr files. 
> The main issue I have experienced is that I am unable to render several representations such as secondary structures because the combined pdb file is missing these records. Is this possibly due to an error on my part? Do you know a way to remedy the situation?
> Thank You,
> Nikolay
> On Mar 23, 2012, at 8:13 PM, "Eric Pettersen" <pett at cgl.ucsf.edu> wrote:
>> On Mar 23, 2012, at 3:30 PM, Nikolay Igorovich Rodionov wrote:
>>> Hi all,
>>> I’m working on a project that requires me to merge models created through PDB BIOMT records. I have been using the copy&combine feature in the model panel to merge all of my models, and then writing a new PDB of only the combined model. I’ve noticed that this method deletes a large amount of information about the structure, including secondary structure records. Is there a way to merge models without losing such data?
>>> If it is relevant, I am merging 90+ models.
>> Hi Nikolay,
>> So, why do you want to preserve the various header records in the merged models?  Chimera will write out appropriate HELIX and SHEET records for your merged structure if you save it in PDB format.
>> I guess I'm pretty unclear as to how to "merge" many of the various record types when combining models.  Such as:  AUTHOR, COMPND, CRYST1, EXPDTA, HEADER, ORIGX, various REMARK records, TITLE, and so on.
>> --Eric
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu

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